Files in Rsamtools

Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

migration_notes.md README.md

NEWS

NAMESPACE

DESCRIPTION

LICENSE

build/vignette.rds

src/as_bam.c

src/bam.c

src/bambuffer.h

src/tabixfile.h

src/zip_compression.h

src/PileupBuffer.h

src/COMPAT_bcf_hdr_read.h

src/idxstats.h

src/ResultManager.cpp

src/idxstats.c

src/tabixfile.c

src/scan_bam_data.c

src/pbuffer_wrapper.h

src/utilities.c

src/tagfilter.h

src/zip_compression.c

src/PosCache.h

src/bambuffer.c

src/bam_mate_iter.cpp

src/BamRangeIterator.h

src/io_sam.c

src/bam_sort.c

src/encode.h

src/fafile.c

src/samtools_patch.c

src/io_sam.h

src/PileupBufferShim.h

src/scan_bam_data.h

src/BamIterator.h

src/utilities.h

src/PosCacheColl.cpp

src/COMPAT_bcf_hdr_read.c

src/BamFileIterator.h

src/fafile.h

src/samtools_patch.h

src/bcffile.c

src/tagfilter.c

src/sam_opts.c

src/PileupBuffer.cpp

src/pileupbam.h

src/bam_plbuf.c

src/pileup.h

src/bam_mate_iter.h

src/ResultManager.h

src/bamfile.c

src/Makevars

src/S4Vectors_stubs.c

src/IRanges_stubs.c

src/XVector_stubs.c

src/R_init_Rsamtools.c

src/bcffile.h

src/pileupbam.c

src/encode.c

src/pileup.cpp

src/sam.c

src/PosCacheColl.h

src/GenomicPosition.h

src/pbuffer_wrapper.cpp

src/as_bam.h

src/bamfile.h

src/Template.h

src/bam_data.c

src/bam_data.h

src/Biostrings_stubs.c

src/sam_utils.c

R/methods-TabixFile.R R/mergeBam.R R/methods-RsamtoolsFileList.R R/idxstatsBam.R R/sortBam.R R/methods-FaFile.R R/scanBcfHeader.R R/testPairedEndBam.R R/methods-RsamtoolsFile.R R/filterBam.R R/io_bam.R R/AllGenerics.R R/quickBamFlagSummary.R R/indexBam.R R/scanBcf.R R/pileup.R R/pkgconfig.R R/methods-BamSampler.R R/utilities.R R/methods-ScanBVcfParam.R R/methods-BamFile.R R/methods-ScanBamParam.R R/asBam.R R/methods-BcfFile.R R/zzz.R R/methods-BamFileList.R R/methods-BamViews.R R/phred2ASCIIOffset.R R/AllClasses.R R/zip_compression.R R/readPileup.R R/methods-PileupFiles.R R/scanBam.R R/methods-ApplyPileupsParam.R R/countBam.R R/scanBamHeader.R

vignettes/Rsamtools-Overview.Rnw

man/zip.Rd man/deprecated.Rd man/applyPileups.Rd man/ApplyPileupsParam-class.Rd man/TabixFile-class.Rd man/headerTabix.Rd man/scanBam.Rd man/defunct.Rd man/indexTabix.Rd man/BcfFile-class.Rd man/FaFile-class.Rd man/quickBamFlagSummary.Rd man/RsamtoolsFileList-class.Rd man/Rsamtools-package.Rd man/testPairedEndBam.Rd man/scanBcf.Rd man/ScanBamParam-class.Rd man/seqnamesTabix.Rd man/RsamtoolsFile-class.Rd man/readPileup.Rd man/scanTabix.Rd man/BamViews-class.Rd man/BamFile-class.Rd man/PileupFiles-class.Rd man/scanFa.Rd man/pileup.Rd man/ScanBcfParam-class.Rd tests/Rsamtools_unit_tests.R

inst/doc/Rsamtools-Overview.Rnw

inst/doc/Rsamtools-Overview.pdf inst/doc/Rsamtools-Overview.R

inst/extdata/example_from_SAM_Spec.bam.bai

inst/extdata/revbins.sam

inst/extdata/tagfilter.sam

inst/extdata/example_from_SAM_Spec.bam

inst/extdata/ex1.bam

inst/extdata/no_which_whole_file.bam.bai

inst/extdata/ex1.vcf.gz.csi

inst/extdata/ce2dict1.fa

inst/extdata/tagfilter.bam

inst/extdata/samtools-github.txt

inst/extdata/tagfilter.bam.bai

inst/extdata/olaps.Rda

inst/extdata/ce2dict1.fa.fai

inst/extdata/example.gtf.gz.tbi

inst/extdata/tiny.bam.bai

inst/extdata/no_which_buffered_pileup.bam.bai

inst/extdata/no_which_buffered_pileup.bam

inst/extdata/revbins.bam.bai

inst/extdata/example_from_SAM_Spec.sam

inst/extdata/ex1.bam.bai

inst/extdata/querybins.bam.bai

inst/extdata/no_which_whole_file.bam

inst/extdata/no_which_buffered_pileup.sam

inst/extdata/tiny.bam

inst/extdata/ex1.sam

inst/extdata/ex1.vcf.gz

inst/extdata/ex1.bcf.gz.csi

inst/extdata/tiny.sam

inst/extdata/example.gtf.gz

inst/extdata/querybins.sam

inst/extdata/querybins.bam

inst/extdata/slxMaq09_urls.txt

inst/extdata/ex1.bcf.gz

inst/extdata/pileup.txt

inst/extdata/revbins.bam

inst/extdata/no_which_whole_file.sam

inst/extdata/tophat/coverage.wig

inst/extdata/tophat/accepted_hits.sam

inst/extdata/tophat/junctions.bed

inst/extdata/tophat/README

inst/scripts/features.R inst/scripts/BamViews-1000g.R

inst/scripts/update-samtools.sh

inst/scripts/remote_test.R inst/unitTests/test_compression.R inst/unitTests/test_TabixFile.R inst/unitTests/test_asBam.R inst/unitTests/test_sortBam_test.R inst/unitTests/test_readPileup.R inst/unitTests/test_FaFile.R inst/unitTests/test_tagfilter.R inst/unitTests/test_bam_header.R inst/unitTests/test_RsamtoolsFile.R inst/unitTests/test_bam.R inst/unitTests/test_phred2ASCIIOffset.R inst/unitTests/test_BamFile.R inst/unitTests/test_pileup_revbins.R inst/unitTests/test_pileup_nowhich.R inst/unitTests/test_pileup_querybins.R inst/unitTests/test_BamViews.R inst/unitTests/test_BcfFile.R inst/unitTests/test_applyPileups.R inst/unitTests/test_pileup_single_range.R inst/unitTests/test_bam_count.R inst/unitTests/test_testPairedEndBam.R inst/unitTests/test_utilities.R inst/unitTests/test_mapqfilter.R inst/unitTests/test_scanBamFlag.R

inst/unitTests/cases/RNEXT.bam

inst/unitTests/cases/ex1_shuf1000.bam

inst/unitTests/cases/plp_refskip.bam.bai

inst/unitTests/cases/no_SAMPLE_header.vcf.gz

inst/unitTests/cases/pileup-no-stars.txt

inst/unitTests/cases/no_header_line.vcf.gz

inst/unitTests/cases/ex1_unsort.bam

inst/unitTests/cases/ex1_shuf1000.bam.bai

inst/unitTests/cases/ex1_zero_index.bam.bai

inst/unitTests/cases/ex1.sam.gz

inst/unitTests/cases/plp_refskip.bam

inst/unitTests/cases/ex1_noindex.bam

Rsamtools documentation built on Nov. 8, 2020, 8:11 p.m.